ped2geno: Convert from 'ped' to 'geno' format

In LEA: LEA: an R package for Landscape and Ecological Association Studies

Description

A function that converts from the ped format to the geno format.

Usage

ped2geno(input.file, output.file = NULL, force = TRUE)

Arguments

input.file	A character string containing a path to the input file, a genotypic matrix in the ped format.
output.file	A character string containing a path to the output file, a genotypic matrix in the geno format. By default, the name of the output file is the same name as the input file with a .geno extension.
force	A boolean option. If FALSE, the input file is converted only if the output file does not exist. If TRUE, convert the file anyway.

Value

output.file

A character string containing a path to the output file, a genotypic matrix in the geno format.

Author(s)

Eric Frichot

See Also

ped geno ancestrymap2lfmm ancestrymap2geno geno2lfmm ped2lfmm vcf2geno lfmm2geno

Examples

# Creation of a file called "example.ped"
# with 4 SNPs for 3 individuals.
data("example_ped")
write.table(example_ped,"example.ped",
    col.names = FALSE, row.names = FALSE, quote = FALSE)

# Conversion    from the ped format ("example.ped") 
#               to the geno format ("example.geno").
# By default,   the name of the output file is the same name 
#               as the input file with a .geno extension.
# Create file:  "example.geno".
output = ped2geno("example.ped")

# Conversion    from the ped format ("example.ped") 
#               to the geno format with the output file called "plop.geno".
# Create file:  "plop.geno".
output = ped2geno("example.ped", "plop.geno")

# As force = false and the file "example.geno" already exists,
# nothing happens.
output = ped2geno("example.ped", force = FALSE)

Example output

	- number of detected individuals:	3
	- number of detected loci:		4


	- number of detected individuals:	3
	- number of detected loci:		4

LEA documentation built on Nov. 8, 2020, 8:19 p.m.